American Black Bear’s Nuclear Family Lineage

June 5, 2015

A recent study from the University of Missouri provides new information about the family lineage and diversification of the American black bear (Ursus americanus) and also revises what we know about their migration patterns before and after the last ice age.

“This is the largest study, both geographically and genomically, of American black bears,” says Emily Puckett, who conducted the study as part of her doctoral work in the lab of Dr. Lori Eggert in the Division of Biological Sciences.

Unlike previous studies that relied on mitochondrial DNA — genetic material that is inherited through the female line — this new study traces the lineage of black bears using the nuclear genome, which includes information from both the female and male lines.

Emily Puckett, Ph.D. ’15

“With information gleaned from the nuclear DNA, we are able to put a finer point on inheritance and lineages,” says Puckett.

Puckett and her colleagues isolated DNA from blood and tissue samples from over 400 black bears across the continental United States, Alaska, and Canada. The samples were collected with the help of 32 state and provincial wildlife agencies, university, and private game outfitter partners. The researchers traced the inheritance of small variations in the DNA code, called single nucleotide polymorphisms (SNPs), to assess the genetic relatedness and gene flow among the bears in their samples.

Their analysis showed that modern black bears are descendants of three distinct lineages. The two main lineages occupy the western and eastern ranges of the North American continent and correspond to eight geographic regions. The third lineage is specific to Alaska. Notably, their analysis showed that black bears from the Alaskan lineage are more closely related to the bears in the Eastern lineage than to bears in the Western lineage, a finding that surprised the researchers.

“You would expect that populations that are geographically close should be genetically close,” says Puckett.

When the researchers dated the lineages, they found that bears from the western lineage split off approximately 67,000 years ago, before the eastern and Alaskan divergence 31,000 years ago. These findings call into question the idea that ice age climate changes alone were responsible for generating diversity in black bears.

“The break off of the western lineage should not be attributed to the Last Glacial Maximum. That was just too far away,” says Puckett. On the other hand, she adds, the split between the Alaskan and eastern lineages may not be fully independent. “The climate was still changing at that time. It’s not unreasonable that the bears were moving to get to good habitat.”

The peak of the last ice age, which occurred around 21,000 years ago, is called the Last Glacial Maximum. Vast ice sheets covered most of the northern continents, including most of North America.
Previous studies have suggested that black bears in the eastern range likely found ice-free habitat somewhere in the broadleaf forests of the east and bears in the western range sought refuge either in the coniferous forests along the Pacific coast or in the near shore islands off modern-day British Columbia. Scientists call these “pockets” of ice-free habitat where plants and animals retreat during ice ages as refugia.

Using a computational method called maximum entropy, Puckett and her colleagues compared the climatic conditions where black bears live today with models of what the climate was like 21,000 years ago to identify four alternative refugia— in the southeast, southwest, Pacific northwest, and Beringia. Refugia in Beringia and the southwest were not previously considered, says Puckett.

According to Puckett, some of the eastern lineage bears that found refuge in the southeast refugium took several migration paths once the ice sheets began to recede.

“At least one of the ancestral populations never leaves the southeast. One starts heading essentially up the Atlantic coast or the Appalachian Mountains, following the forest as they’re expanding towards the northeast, and then continues counterclockwise around the Great Lakes landform,” explains Puckett. “Simultaneously, some bears taking off around the Gulf Coast, find the lush Mississippi Valley, follow the river, which eventually opens up into huge amounts of forested land that we see in the Ozarks and the Ouachita Mountains.”

According to patterns in the nuclear DNA, by about 11,000 years ago, the black bears that ended up in the forests of the Central Interior Highlands became one of the geographic regions of the Eastern lineage. This further divergence of the Eastern lineage following the ice age, says Puckett, is evidence of diversification by range expansion.

The bears from the Alaskan lineage were pushed into the Beringial refugium. When the ice receded, Puckett says, these bears spread out across Alaska but also started moving down the Pacific coast and then north around the Yukon Mountains to get out into Canada.

“That’s the route that they might have taken so that we see these admixture relationships between Alaska and Eastern lineage bears in the Great Lakes and the northeast,” says Puckett.

While the Alaskan bears went up and over the Rocky Mountains and eventually met up with the Eastern lineage bears, Puckett believes the Rockies trapped bears in the southwest refugium in Mexico and in the southern Rockies, along with a number of other plant and animal species.

“When you look at the phylogeography of other species that have both northern and southern Rocky distributions, we see this really strong pattern of genetic differentiation between the northern and southern Rockies,” says Puckett. “We see this same genetic separation in black bears as well.”

Understanding the lineage of black bears from the perspective of the nuclear genome has advantages beyond just recreating their genealogical history.

“What’s exciting about the results of this study is that we now understand how bears are related across different geographical ranges and we can utilize this information to begin understanding functional adaptations such as hibernation characteristics,” Puckett says.

The study also will help inform conservation management teams across state lines and even across countries including, Canada, the U.S. and Mexico.